Development of a Brassica seed cDNA microarray

Genome ◽  
2008 ◽  
Vol 51 (3) ◽  
pp. 236-242 ◽  
Author(s):  
Daoquan Xiang ◽  
Raju Datla ◽  
Fengling Li ◽  
Adrian Cutler ◽  
Meghna R. Malik ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Cdna Array ◽  
Brassica Species ◽  
Crop Species ◽  
Rna Targets ◽  
Associated Functions ◽  
Leaf Tissues ◽  
Germinating Seeds ◽  
Signal Intensities

Brassica species represent several important crops including canola ( Brassica napus ). Understanding of genetic elements that contribute to seed-associated functions will impact future improvements in the canola crop. Brassica species share a very close taxonomic and molecular relationship with Arabidopsis thaliana. However, there are several subtle but distinct seed-associated agronomic characteristics that differ among the oil seed crop species. To address these, we have generated 67 535 ESTs predominately from Brassica seeds, analyzed these sequences, and identified 10 642 unigenes for the preparation of a targeted seed cDNA array. A set of 10 642 PCR primer pairs was designed and corresponding amplicons were produced for spotting, along with relevant controls. Critical quality control tests produced satisfactory results for use of this microarray in biological experiments. The microarray was also tested with specific RNA targets from embryos, germinating seeds, and leaf tissues. The hybridizations, signal intensities, and overall quality of these slides were consistent and reproducible. Additionally, there are 429 ESTs represented on the array that show no homology with any A. thaliana annotated gene or any gene in the Brassica genome databases or other plant databases; however, all of these probes hybridized to B. napus transcripts, indicating that the array also will be useful in defining expression patterns for genes so far unique to Brassica species.

AN IMPROVED METHOD FOR INHIBITOR FREE NUCLEIC ACIDS FROM POLYPHENOL RICH LEAVES OF MUSA SPP

2017 ◽  
Vol 23 (1) ◽  
Author(s):  
N.NANDHA KUMAR ◽  
K. SOURIANATHA SUNDARAM ◽  
D. SUDHAKAR ◽  
K.K. KUMAR
Keyword(s):  
Polymerase Chain Reaction ◽  
Quantitative Polymerase Chain Reaction ◽  
Proteinase K ◽  
Chain Reaction ◽  
Banana Plant ◽  
High Molecular Weight Dna ◽  
Musa Spp ◽  
Leaf Tissues ◽  
Polymerase Chain

Excessive presence of polysaccharides, polyphenol and secondary metabolites in banana plant affects the quality of DNA and it leads to difficult in isolating good quality of DNA. An optimized modified CTAB protocol for the isolation of high quality and quantity of DNA obtained from banana leaf tissues has been developed. In this protocol a slight increased salt (NaCl) concentration (2.0M) was used in the extraction buffer. Polyvinylpyrrolidone (PVP) and Octanol were used for the removal of polyphenols and polymerase chain reaction (PCR) inhibitors. Proteins like various enzymes were degraded by Proteinase K and removed by centrifugation from plant extract during the isolation process resulting in pure genomic DNA, ready to use in downstream applications including PCR, quantitative polymerase chain reaction (qPCR), ligation, restriction and sequencing. This protocol yielded a high molecular weight DNA isolated from polyphenols rich leaves of Musa spp which was free from contamination and colour. The average yields of total DNA from leaf ranged from 917.4 to 1860.9 ng/ìL. This modified CTAB protocol reported here is less time consuming 4-5h, reproducible and can be used for a broad spectrum of plant species which have polyphenol and polysaccharide compounds.

scholarly journals Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in Rice

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1154
Author(s):  
Hongjia Zhang ◽  
Seong-Gyu Jang ◽  
San Mar Lar ◽  
Ah-Rim Lee ◽  
Fang-Yuan Cao ◽  
...  
Keyword(s):  
Gene Family ◽  
Catalytic Domain ◽  
Amylose Content ◽  
Expression Patterns ◽  
Starch Synthase ◽  
Eating Quality ◽  
Segmental Duplications ◽  
Genome Wide ◽  
The Relationship

Starch is a major ingredient in rice, and the amylose content of starch significantly impacts rice quality. OsSS (starch synthase) is a gene family related to the synthesis of amylose and amylopectin, and 10 members have been reported. In the present study, a synteny analysis of a novel family member belonging to the OsSSIV subfamily that contained a starch synthase catalytic domain showed that three segmental duplications and multiple duplications were identified in rice and other species. Expression data showed that the OsSS gene family is involved in diverse expression patterns. The prediction of miRNA targets suggested that OsSS are possibly widely regulated by miRNA functions, with miR156s targeted to OsSSII-3, especially. Haplotype analysis exhibited the relationship between amylose content and diverse genotypes. These results give new insight and a theoretical basis for the improved amylose content and eating quality of rice.

Carboxylesterase overexpression in the male reproductive tract: a universal safeguarding mechanism?

1999 ◽  
Vol 11 (3) ◽  
pp. 133 ◽  
Author(s):  
A. T. Mikhailov ◽  
M. Torrado
Keyword(s):  
Reproductive Tract ◽  
Expression Patterns ◽  
Cell Lineage ◽  
Environmental Chemicals ◽  
Male Reproductive Tract ◽  
Morphological Organization ◽  
Associated Functions ◽  
And Function ◽  
Hypothetical Explanation

Data on expression patterns of carboxylesterases in the male reproductive tract of different animal groups (i.e. bivalve mollusks, fruitflies and rodents) are summarized to highlight some particularly interesting questions in the context of sperm differentiation, maturation and function. The male reproduc-tive system, in spite of extreme variation in the anatomical/morphological organization in different species, is characterized by similar patterns of male-dependent carboxylesterase overexpression. The phenomenon of conserved carboxylesterase overexpression indicates similar male sex-associated functions of the enzymes. There is possible evidence of carboxylesterase recruitment by male reproductive-tract tissues indi-cating that it could be adaptive for spermatogenesis, sperm maturation and sperm use. Moreover, this idea can be extended to include a sperm cell lineage protection. This issue is discussed in the light of recent data on environmental reproductive xenobiotics that can provide a basis for a hypothetical explanation of car-boxylesterase overexpression in the male reproductive tract. Based on a well-known role of car-boxylesterases in detoxification of environmental chemicals such as organophosphate pesticides, it is proposed that various male genital tract carboxylesterases may be characterized by a similar physiological function to protect the male reproductive system against xenobiotic influences that could provoke its dys-function, thus altering sperm differentiation and maturation.

scholarly journals ВПЛИВ ТЕХНОЛОГІЧНИХ ПРИЙОМІВ ВИРОЩУВАННЯ НА ФОРМУВАННЯ ПОКАЗНИКІВ ЯКОСТІ ЗЕРНА ПШЕНИЦІ ОЗИМОЇ В УМОВАХ ПІВНІЧНОГО СТЕПУ

2014 ◽  
pp. 67-73
Author(s):  
В. І. Козечко
Keyword(s):  
Protein Content ◽  
High Protein ◽  
Seeding Rate ◽  
High Protein Content ◽  
The Third ◽  
Maximum Productivity ◽  
Germinating Seeds ◽  
Spring Rape

Результати проведених експериментальних дослі-джень свідчать, що за вирощування різних сортівпшениці озимої після ріпаку ярого в умовах північногоСтепу України одержання найбільш якісного зерна(третього класу якості) забезпечує сівба 25 вереснята 5 жовтня. Сівба 5 та 15 вересня забезпечувалаодержання зерна, здебільшого, п’ятого й четвертогокласів якості. Із-поміж досліджуваних сортів пше-ниці озимої найбільшим вмістом білку (11,2–13,0 %) іклейковини (17,5–22,7 %) у зерні вирізнявся сорт Се-лянка. Найменшими ці показники були у сорту Подо-лянка – 10,6–12,5 та 17,1–21,9 % відповідно. Об¢ємхліба, отриманого з борошна пшениці озимої сортуСелянка, був найвищим. Так, у середньому за 2008–2010 рр. він коливався від 495 см3 за сівби 5 вереснянормою висіву 4 млн схожих насінин/га до 612 см3 засівби 5 жовтня цією ж нормою. Встановлено впливнорм висіву насіння на показники якості зерна. Так,найвищий вміст білку і клейковини в зерні, а такожоб’єм хліба відмічено на варіантах досліду, де сівбупроводили нормою 4 млн схожих насінин/га. Збіль-шення норми висіву призводило до зменшення данихпоказників. У середньому за роки досліджень найвищуврожайність формував сорт Селянка (4,89 т/га) засівби 25 вересня нормою 5 млн схожих насінин/га.Максимальну врожайність рослини сорту Золотоко-лоса – 4,20 та 4,19 т/га – формували, відповідно, засівби 5 жовтня нормою 6 млн схожих насінин/га та 25вересня нормою висіву 5 млн схожих насінин/га. Най-нижчу серед сортів урожайність формував сортПодолянка, що коливалася за період проведення до-сліджень у межах 2,99–3,75 т/га. Results of the conducted pilot researches testify that at cultivation of various sorts of wheat winter after a spring rape in the conditions of the northern Steppe of Ukraine, receiving the most qualitative grain, the third class of quality, provides sowing on 25 September and on 5 October. Sowing on 5 and 15 September provided grain, generally the fifth and fourth classes of quality. Among sorts of wheat winter which were studied in the experiences, the greatest protein content (11,2–13,0%) and glutens (17,5–22,7%) in grain Selyank's sort differed. The smallest Podolyank's sort of – 10,6–12,5 and 17,1–21,9% had these indicators respectively. The volume of the bread received from a flour of wheat of winter of a sort of Selyanka, was the highest. So, on the average for 2008–2010 it fluctuated from 495 cm3 when sowing on 5 September seeding rate of 4 million units germinating seeds/ha to 612 cm3 when sowing on 5 October the same norm. Influence of seeding rate on indicators of quality of grain is established. So, high protein content and glutens in grain, and also the volume of bread are noted on experience options where sowing carried out norm of 4 million units germinating seeds/ha. The increase in seeding rate led to reduction of these indicators. Average, over years of research, the highest yield sort Selyanka formed (4,89 t per ha) when sowing on 25 September norm of 5 million units germinating seeds/ha. The maximum productivity of a plant of a grade of Zolotokolosa – 4,20 and 4,19 t per ha formed, respectively, when sowing on 5 October norm of 6 million units germinating seeds/ha and on 25 September seeding rate of 5 million units germinating seeds/ha. The low among grades productivity was formed by a sort of Podolyanka at which it fluctuated, during carrying out researches, within 2,99–3,75 t per ha.

scholarly journals Convergence of Bar and Cry1Ac Mutant Genes in Soybean Confers Synergistic Resistance to Herbicide and Lepidopteran Insects

2021 ◽  
Vol 12 ◽  
Author(s):  
Tien Dung Nguyen ◽  
Van Hien La ◽  
Van Duy Nguyen ◽  
Tri Thuc Bui ◽  
Thi Tinh Nguyen ◽  
...  
Keyword(s):  
Transgenic Plants ◽  
Larval Mortality ◽  
Expression Patterns ◽  
Herbicide Tolerance ◽  
Field Tests ◽  
Phenotypic Traits ◽  
Gene Stacking ◽  
Transgenic Soybean ◽  
Crop Species ◽  
Lepidopteran Insects

Soybean is a globally important crop species, which is subject to pressure by insects and weeds causing severe substantially reduce yield and quality. Despite the success of transgenic soybean in terms of Bacillus thuringiensis (Bt) and herbicide tolerance, unforeseen mitigated performances have still been inspected due to climate changes that favor the emergence of insect resistance. Therefore, there is a need to develop a biotech soybean with elaborated gene stacking to improve insect and herbicide tolerance in the field. In this study, new gene stacking soybean events, such as bialaphos resistance (bar) and pesticidal crystal protein (cry)1Ac mutant 2 (M#2), are being developed in Vietnamese soybean under field condition. Five transgenic plants were extensively studied in the herbicide effects, gene expression patterns, and insect mortality across generations. The increase in the expression of the bar gene by 100% in the leaves of putative transgenic plants was a determinant of herbicide tolerance. In an insect bioassay, the cry1Ac-M#2 protein tested yielded higher than expected larval mortality (86%), reflecting larval weight gain and weight of leaf consumed were less in the T1 generation. Similarly, in the field tests, the expression of cry1Ac-M#2 in the transgenic soybean lines was relatively stable from T0 to T3 generations that corresponded to a large reduction in the rate of leaves and pods damage caused by Lamprosema indicata and Helicoverpa armigera. The transgenic lines converged two genes, producing a soybean phenotype that was resistant to herbicide and lepidopteran insects. Furthermore, the expression of cry1Ac-M#2 was dominant in the T1 generation leading to the exhibit of better phenotypic traits. These results underscored the great potential of combining bar and cry1Ac mutation genes in transgenic soybean as pursuant of ensuring resistance to herbicide and lepidopteran insects.

scholarly journals Glucosinolate Profile and Glucosinolate Biosynthesis and Breakdown Gene Expression Manifested by Black Rot Disease Infection in Cabbage

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1121
Author(s):  
Mehede Hassan Rubel ◽  
Md. Abuyusuf ◽  
Ujjal Kumar Nath ◽  
Arif Hasan Khan Robin ◽  
Hee Jeong Jung ◽  
...  
Keyword(s):  
Gene Expression ◽  
Xanthomonas Campestris ◽  
Defense Mechanism ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Brassica Species ◽  
Black Rot ◽  
Clear Understanding ◽  
Knock Out ◽  
Rot Disease

Cabbage (Brassica oleracea var. capitata) is an economically important crop in the family Brassicaceae. Black rot disease is a top ranked cabbage disease, which is caused by Xanthomonas campestris pv. campestris (Xcc) and may reduce 50% crop loss. Therefore, we need a clear understanding of black rot disease resistance for sustainable disease management. The secondary metabolites, like Glucosinolate (GSL) presents in Brassica species, which plays a potential role in the defense mechanism against pathogens. However, there is little known about GSL-regulated resistance mechanisms and GSL biosynthesis and the breakdown related gene expression after black rot disease infection in cabbage. In this study, relative expression of 43 biosynthetic and breakdown related GSLs were estimated in the black rot resistant and susceptible cabbage lines after Xcc inoculation. Ten different types of GSL from both aliphatic and indolic groups were identified in the contrasting cabbage lines by HPLC analysis, which included six aliphatic and four indolic compounds. In the resistant line, nine genes (MYB122-Bol026204, MYB34-Bol017062, AOP2-Bo9g006240, ST5c-Bol030757, CYP81F1-Bol017376, CYP81F2-Bol012237, CYP81F4-Bol032712, CYP81F4-Bol032714 and PEN2-Bol030092) showed consistent expression patterns. Pearson’s correlation coefficient showed positive and significant association between aliphatic GSL compounds and expression values of ST5c-Bol030757 and AOP2-Bo9g006240 genes as well as between indolic GSL compounds and the expression of MYB34-Bol017062, MYB122-Bol026204, CYP81F2-Bol012237, CYP81F4-Bol032712 and CYP81F4-Bol032714 genes. This study helps in understanding the role of GSL biosynthesis and breakdown related genes for resistance against black rot pathogen in cabbage, which could be further confirmed through functional characterization either by overexpression or knock-out mutation.

Transcriptome profile and association study revealed STAT3 gene as a potential quality marker of bovine gametes

Zygote ◽  
2020 ◽  
Vol 28 (2) ◽  
pp. 116-130
Author(s):  
Nasser Ghanem ◽  
Dessie Salilew-Wondim ◽  
Michael Hoelker ◽  
Karl Schellander ◽  
Dawit Tesfaye
Keyword(s):  
Estrous Cycle ◽  
Semen Quality ◽  
Sperm Quality ◽  
Expression Patterns ◽  
Cdna Array ◽  
Transcript Abundance ◽  
Low Fertility ◽  
High Fertility ◽  
Nucleotide Polymorphisms ◽  
Genetic Merit

SummaryThe present study was aimed to investigate differences in molecular signatures in oocytes derived from Holstein-Friesian heifers with different genetic merit for fertility, euthanized during day 0 or day 12 of the estrous cycle. Moreover, association between single nucleotide polymorphisms (SNPs) of ODC1 and STAT3 genes and bull fertility traits was investigated. The gene expression patterns were analyzed using cDNA array and validated with quantitative real-time polymerase chain reaction (PCR). The result revealed that several genes have shown not only to be regulated by fertility merit but also by the day of oocyte recovery during the estrous cycle. The STAT3 gene was found to be upregulated in oocytes recovered from animals with high fertility merit at both day 0 and day 12. Some other genes like PTTG1, ODC1 and TUBA1C were downregulated at day 0 and upregulated at day 12 in high, compared with low, fertility merit recovered oocytes. In contrast, the transcript abundance of TPM3 was upregulated at day 0 and downregulated at day 12 in high, compared with low, fertility merit recovered oocytes. In addition, ODC1 and STAT3 were found to be associated (P < 0.05) with sperm quality traits as well as flow cytometry parameters. Therefore, the expression of several candidate genes including ODC1 and STAT3 was related to the genetic merit of the cow. In addition polymorphisms in these two genes were found to be associated with bull semen quality.

scholarly journals The Correct Cover Crop Species Integrated with Slurry Can Increase Biomass, Quality and Nitrogen Cycling to Positively Affect Yields in a Subsequent Spring Barley Rotation

Agronomy ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1760
Author(s):  
Paul Cottney ◽  
Lisa Black ◽  
Ethel White ◽  
Paul N. Williams
Keyword(s):  
Cover Crops ◽  
Cover Crop ◽  
Crop Yields ◽  
Spring Barley ◽  
C:N Ratio ◽  
Brassica Species ◽  
Carbon Accumulation ◽  
Soil Mineral Nitrogen ◽  
Crop Species ◽  
N Accumulation

The aim of this study is to identify species of cover crops that cause an increase in biomass and total nutrient accumulation in response to manure/slurry. This could improve nutrient efficiency and intensify the benefits from over-winter cover crops in arable rotations and improve following commercial crop yields. In a pot experiment, sixteen cover crops were grown for 100 days in response to slurry. Growth and nutrient (N, P, K, Mg and S) accumulation were measured, and then residue was reincorporated into the soil with spring barley (Hodeum vulgare L.) sown and harvested for yield. In response to slurry, tillage radish (Raphanus sativus L.) increased N accumulation by 101% due to a significant increase in biomass and % N (p < 0.05) over its relative control plots. Significant interactions between species and the application of slurry were found in cover crop biomass, cover crop and spring barley nutrient uptake, as well as cover crop carbon accumulation, particularly in the brassica species used. Slurry integrated with cover crops both reduced the cover crop C:N ratio and enhanced nutrient cycling compared to the control when soil mineral nitrogen (SMN) and spring barley crop N offtake were pooled. However, this was not observed in the legumes. This study shows that slurry integration with cover crops is a promising sustainable farming practice to sequester N and other macro-nutrients whilst providing a range of synergistic benefits to spring barley production when compared to unplanted/fallow land rotations. However, this advantage is subject to use of responsive cover crop species identified in this study.

The mosaic of ancestral karyotype blocks in the Sinapis alba L. genome

Genome ◽  
2011 ◽  
Vol 54 (1) ◽  
pp. 33-41 ◽  
Author(s):  
Matthew N. Nelson ◽  
Isobel A.P. Parkin ◽  
Derek J. Lydiate
Keyword(s):  
Genetic Research ◽  
Brassica Species ◽  
Sinapis Alba ◽  
Ancestral Karyotype ◽  
Crop Species ◽  
B Genome ◽  
A Genome ◽  
The Rich ◽  
Conserved Gene ◽  
First Time

The organisation of the Sinapis alba genome, comprising 12 linkage groups (n = 12), was compared with the Brassicaceae ancestral karyotype (AK) genomic blocks previously described in other crucifer species. Most of the S. alba genome falls into conserved triplicated genomic blocks that closely match the AK-defined genomic blocks found in other crucifer species including the A, B, and C genomes of closely related Brassica species. In one instance, an S. alba linkage group (S05) was completely collinear with one AK chromosome (AK1), the first time this has been observed in a member of the Brassiceae tribe. However, as observed for other members of the Brassiceae tribe, ancestral genomic blocks were fragmented in the S. alba genome, supporting previously reported comparative chromosome painting describing rearrangements of the AK karyotype prior to the divergence of the Brassiceae from other crucifers. The presented data also refute previous phylogenetic reports that suggest S. alba was more closely related to Brassica nigra (B genome) than to B. rapa (A genome) and B. oleracea (C genome). A comparison of the S. alba and Arabidopsis thaliana genomes revealed many regions of conserved gene order, which will facilitate access to the rich genomic resources available in the model species A. thaliana for genetic research in the less well-resourced crop species S. alba.

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